########
# Usage: Rscript detail_circRNA_boxplot1.R 'exo_circ_001570' "TRUE" "Healthy,Benign,BRCA,HCC"
#        Rscript detail_circRNA_boxplot1.R 'exo_circ_001570' "FALSE" "Healthy,Benign,BRCA,HCC"

# 传入参数： target = 'exo_circ_001570'  
#            log = "TRUE"                   # log = "FALSE"   or   log = "TRUE"
#            cohort.selected = c('Healthy', 'Benign', 'BRCA', 'HCC')

# 默认传入所有的cohorts
#        Rscript detail_circRNA_boxplot1.R 'exo_circ_001570' "TRUE" "Urine,Bile,CSF,Healthy,Benign,BRCA,CHD,CRC,GC,HCC,KIRC,ML,OV,PAAD,SCLC"
#        Rscript detail_circRNA_boxplot1.R 'exo_circ_001570' "FALSE" "Urine,Bile,CSF,Healthy,Benign,BRCA,CHD,CRC,GC,HCC,KIRC,ML,OV,PAAD,SCLC"
#
########
library(ggplot2)
library(ggpubr)
library(RColorBrewer)

library(optparse)

option_list <- list(
  make_option("--t", default = "", type = "character", help = "target"),
  make_option("--i", default = "", type = "character", help = "target file"),
  make_option("--l", default = "", type = "character", help = "log"),
  make_option("--c", default = "", type = "character", help = "cohort selected"),
  make_option("--o", default = "", type = "character", help = "output png file")
)
opt <- parse_args(OptionParser(option_list = option_list))

Args = commandArgs()
target = opt$t
log =opt$l
cohort.selected = opt$c
cohort.selected = as.vector(unlist(strsplit(cohort.selected, ',')))

# target = 'exo_circ_031140'
# log = "TRUE"                   # log = "FALSE"   or   log = "TRUE"
# cohort.selected = c('Healthy', 'Benign', 'BRCA', 'HCC', 'SCLC')
# cohort.selected = c("Urine","Bile","CSF","Healthy","Benign","BRCA","CHD","CRC","GC","HCC","KIRC","ML","OV","PAAD","SCLC")
# path = "D:\\exo\\905\\submit 7\\detail_circRNA"
# setwd(path)
  
targetType = 'circRNA'
w=12
h=6
outfile = opt$o

infile =opt$i
data.target = read.csv(infile, sep=',', header = 1, row.names = NULL)
colnames(data.target) = c('sample', 'type', 'cohort', 'sampleSize','TPM')                  ### sampleSize
data.target = data.target[data.target$cohort %in% cohort.selected, ]
data.target$label = paste(data.target$cohort, '\n', '(', data.target$sampleSize,')', sep='')   ### label

cohortsNumber = length(cohort.selected)
if(cohortsNumber==15){               ### 默认选择除（ESCC, GBM, MEL）外的所有cohort， 且固定cohort顺序
  labelOrder = c("Urine\n(16)","CSF\n(5)","Bile\n(15)","Healthy\n(118)","Benign\n(130)","BRCA\n(140)","CHD\n(12)","CRC\n(35)","GC\n(9)","HCC\n(112)","KIRC\n(15)","ML\n(28)","OV\n(30)","PAAD\n(164)","SCLC\n(36)")
  data.target$label = factor(data.target$label, levels = labelOrder)
}

cols = c(brewer.pal(9,"Pastel1"), brewer.pal(9,"Set3"))
if(log == "FALSE"){
  pdf(outfile,  width=w, height=h)
  p = ggplot(data.target, aes(x = label, y = TPM, fill=label))+
    geom_boxplot(linetype = "dashed", width=0.6, outlier.shape = 1, outlier.size = 0.8, outlier.colour = 'black', color="#525252", size=0.5) +
    stat_boxplot(aes(ymin = ..lower.., ymax = ..upper..), width=0.6, outlier.shape = 1, outlier.size = 0.8, outlier.colour = 'black', color="#525252", size=0.5) +
    stat_boxplot(geom = "errorbar", aes(ymin = ..ymax..), color="#525252", size=0.5, width=0.3) +
    stat_boxplot(geom = "errorbar", aes(ymax = ..ymin..), color="#525252", size=0.5, width=0.3)+
    scale_fill_manual(values = cols)+
    xlab('')+ ylab('CPM')+
    ggtitle(target)+
    theme_bw() + 
    theme(panel.grid.major.x = element_blank(),
          panel.grid= element_line(colour = 'gray'))+
    theme(axis.title = element_text(size = 12, face = "bold"))+
    theme(plot.title = element_text(size = 14, face = "bold", hjust = 0.5))+
    guides(fill = FALSE, colour = FALSE)+
    theme(panel.border = element_rect(linetype = 'solid', size = 1.2,fill = NA),
          axis.text.y = element_text(face = 'bold',color = 'black',size = 10, angle = 360),
          axis.text.x = element_text(face = 'bold',color = 'black',size = 10, angle = 360, hjust = 0.5),
          axis.title = element_text(size = 14, face = "bold"))
}else{
  data.target$TPM = log2(data.target$TPM+1)
  pdf(outfile,  width=w, height=h)
  p = ggplot(data.target, aes(x = label, y = TPM, fill=label))+
    geom_boxplot(linetype = "dashed", width=0.6, outlier.shape = 1, outlier.size = 0.8, outlier.colour = 'black', color="#525252", size=0.5) +
    stat_boxplot(aes(ymin = ..lower.., ymax = ..upper..), width=0.6, outlier.shape = 1, outlier.size = 0.8, outlier.colour = 'black', color="#525252", size=0.5) +
    stat_boxplot(geom = "errorbar", aes(ymin = ..ymax..), color="#525252", size=0.5, width=0.3) +
    stat_boxplot(geom = "errorbar", aes(ymax = ..ymin..), color="#525252", size=0.5, width=0.3)+
    scale_fill_manual(values = cols)+
    xlab('')+ ylab('log2(CPM+1)')+
    ggtitle(target)+
    theme_bw() + 
    theme(panel.grid.major.x = element_blank(),
          panel.grid= element_line(colour = 'gray'))+
    theme(axis.title = element_text(size = 12, face = "bold"))+
    theme(plot.title = element_text(size = 14, face = "bold", hjust = 0.5))+
    guides(fill = FALSE, colour = FALSE)+
    theme(panel.border = element_rect(linetype = 'solid', size = 1.2,fill = NA),
          axis.text.y = element_text(face = 'bold',color = 'black',size = 10, angle = 360),
          axis.text.x = element_text(face = 'bold',color = 'black',size = 10, angle = 360, hjust = 0.5),
          axis.title = element_text(size = 14, face = "bold"))
}
print(p)
dev.off()  





